Minor-Variant-Phasing-Tool

Minor-Variant-Phasing-Tool for Pacbio data

Input

• Bam file: Bam file should be generated by Pacbio blasr program with CCS reads.
  The CCS sequences for alignment: 10 full pass, barcode quality of >= 45, predicted read accuracy >= 0.99.

• Reference file: Fasta format.

• SNPs file: csv records, with first column records segment name, second for position, third for Ref nucleotide and the fourth for Alt nucleotide. Like below:

  CHROM	POS	REF	ALT
  Brisbane_PB1_codon_mutant	4	G	A
  Brisbane_M_codon_mutant_	92	G	C
  brisbane_NS_codon_mutant	100	A	G

Output

• Phasing graph in jpeg format.

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